Local magnification effects and trajectory overlaps related to the presence of a second phase (clusters) are key problems and still open issues in the assessment of quantitative composition data in three-dimensional atom probe tomography (APT) particularly for tiny solute-enriched clusters. A model based on the distribution of distance of first nearest neighbor atoms has been developed to exhibit the variations in the apparent atomic density in reconstructed volumes and to correct compositions that are biased by local magnification effects. This model was applied to both simulated APT reconstructions and real experimental data and shows an excellent agreement with the expected composition of clusters.